source: issm/oecreview/Archive/19101-20495/ISSM-19626-19627.diff

Last change on this file was 20498, checked in by Mathieu Morlighem, 9 years ago

CHG: done with Archive/19101-20495
File size: 13.9 KB

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/DakotaDev.cmake.patch

     
     15,8c5,8
     2< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build")
     3< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL
     4<   "Enable DAKOTA specification maintenance mode?")
     5< set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?")
     6---
     7> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build")
     8> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL
     9> #  "Enable DAKOTA specification maintenance mode?")
     10> #set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?")
     1114c14
     12< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE)
     13---
     14> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE)

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/ParallelLibrary.cpp.patch

     
     151a54,76
     2> /** This constructor is provided for the ISSM software, to run serial
     3>  * Dakota in a parallel MPI ring: */
     4> ParallelLibrary::ParallelLibrary(char* serial_mode):
     5>         mpiManager(dummy_mpi_mgr), programOptions(dummy_prg_opt),
     6>           outputManager(dummy_out_mgr), dummyFlag(true), outputTimings(false)
     7> {
     8>   initialize_timers();
     9>
     10>   // do not initialize MPI.  Get worldRank/worldSize if available
     11>   ParallelLevel pl;
     12> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota!
     13>   pl.serverIntraComm = MPI_COMM_NULL;
     14>   Cout << "Running Dakota 6.1 MPI executable in serial mode on CPU 0 for ISSM." << std::endl;
     15> #else // mpi not available
     16>   pl.serverIntraComm = MPI_COMM_NULL;
     17>   Cout << "Running Dakota 6.1 serial executable in serial mode for ISSM." << std::endl;
     18> #endif // HAVE_MPI
     19>
     20>   parallelLevels.push_back(pl);
     21>   increment_parallel_configuration();
     22> }
     23>
     24>

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/NonDLocalReliability.cpp.patch

     
     12645a2646
     2>                // add sensitivity output to importance factors (jes, 8/06/10)
     32651c2652,2655
     4<           << std::setw(width) << impFactor(j,i) << '\n';
     5---
     6>           << std::setw(width) << impFactor(j,i)
     7>                << "  Sensitivity = "
     8>                << std::resetiosflags(std::ios::adjustfield)
     9>                << std::setw(width) << fnGradsMeanX(j,i) << '\n';

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/CMakeLists.txt.pfe.patch

     
     1156c153,155
     2< # TODO: Can't this be integrated into the following logic?
     3---
     4> # TODO: Can't this be integrated into the following logic?
     5> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread")
     6> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread")

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/ParallelLibrary.hpp.patch

     
     1475a476,477
     2>   /// library mode constructor, serial mode (for the ISSM software)
     3>   ParallelLibrary(char* serial_mode);

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/BuildDakotaCustom.cmake.yosemite.patch

     
     167a68,75
     2> set( DAKOTA_HAVE_MPI ON
     3>  CACHE BOOL "Always build with MPI enabled" FORCE)
     4> set( MPI_INCLUDE_PATH
     5>  "$ENV{ISSM_DIR}/externalpackages/mpich/install/include"
     6>  CACHE FILEPATH "Use installed MPI headers" FORCE)
     7> set( MPI_LIBRARY
     8>  "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.a"
     9>  CACHE FILEPATH "Use installed MPI library" FORCE)
     1073,77c73,77
     11< #set(BOOST_ROOT
     12< #    "path/to/custom/Boost/install/directory"
     13< #    CACHE PATH "Use non-standard Boost install" FORCE)
     14< #set( Boost_NO_SYSTEM_PATHS TRUE
     15< #     CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE)
     16---
     17> set(BOOST_ROOT
     18>     "$ENV{ISSM_DIR}/externalpackages/boost/install"
     19>     CACHE PATH "Use non-standard Boost install" FORCE)
     20> set( Boost_NO_SYSTEM_PATHS TRUE
     21>      CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE)
     2291,93c91,93
     23< #set( CMAKE_INSTALL_PREFIX
     24< #     "/path/to/Dakota/installation"
     25< #     CACHE PATH "Path to Dakota installation" )
     26---
     27> set( CMAKE_INSTALL_PREFIX
     28>      "$ENV{ISSM_DIR}/externalpackages/dakota/install"
     29>      CACHE PATH "Path to Dakota installation" )

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/NonDSampling.cpp.patch

     
     1780,786c780,787
     2<   if (!subIteratorFlag) {
     3<     nonDSampCorr.compute_correlations(vars_samples, resp_samples);
     4<     // archive the correlations to the results DB
     5<     nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels,
     6<                                     div_labels, dsv_labels, drv_labels,
     7<                                     iteratedModel.response_labels());
     8<   }
     9---
     10> //don't compute for now, too expensive.
     11> //  if (!subIteratorFlag) {
     12> //   nonDSampCorr.compute_correlations(vars_samples, resp_samples);
     13> //    // archive the correlations to the results DB
     14> //    nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels,
     15> //                                  div_labels, dsv_labels, drv_labels,
     16> //                                  iteratedModel.response_labels());
     17> //  }
     181277,1278c1278,1281
     19<     nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels,
     20<                                   drv_labels,iteratedModel.response_labels());
     21---
     22>
     23> //don't output for now.
     24> //    nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels,
     25> //                                drv_labels,iteratedModel.response_labels());

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/BuildDakotaCustom.cmake.mac.patch

     
     191,93c91,93
     2< #set( CMAKE_INSTALL_PREFIX
     3< #     "/path/to/Dakota/installation"
     4< #     CACHE PATH "Path to Dakota installation" )
     5---
     6> set( CMAKE_INSTALL_PREFIX
     7>      "$ENV{ISSM_DIR}/externalpackages/dakota/install"
     8>      CACHE PATH "Path to Dakota installation" )

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/BuildDakotaCustom.cmake.patch 

    Property changes on: ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/BuildDakotaCustom.cmake.mac.patch
___________________________________________________________________
Added: svn:executable
   + *
     
     167a68,75
     2> set( DAKOTA_HAVE_MPI ON
     3>  CACHE BOOL "Always build with MPI enabled" FORCE)
     4> set( MPI_INCLUDE_PATH
     5>  "$ENV{ISSM_DIR}/externalpackages/mpich/install/include"
     6>  CACHE FILEPATH "Use installed MPI headers" FORCE)
     7> set( MPI_LIBRARY
     8>  "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so"
     9>  CACHE FILEPATH "Use installed MPI library" FORCE)
     1073,77c73,77
     11< #set(BOOST_ROOT
     12< #    "path/to/custom/Boost/install/directory"
     13< #    CACHE PATH "Use non-standard Boost install" FORCE)
     14< #set( Boost_NO_SYSTEM_PATHS TRUE
     15< #     CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE)
     16---
     17> set(BOOST_ROOT
     18>     "$ENV{ISSM_DIR}/externalpackages/boost/install"
     19>     CACHE PATH "Use non-standard Boost install" FORCE)
     20> set( Boost_NO_SYSTEM_PATHS TRUE
     21>      CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE)
     2291,93c91,93
     23< #set( CMAKE_INSTALL_PREFIX
     24< #     "/path/to/Dakota/installation"
     25< #     CACHE PATH "Path to Dakota installation" )
     26---
     27> set( CMAKE_INSTALL_PREFIX
     28>      "$ENV{ISSM_DIR}/externalpackages/dakota/install"
     29>      CACHE PATH "Path to Dakota installation" )

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/CMakeLists.txt.patch

     
     147a48,50
     2> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE)
     3> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE)
     4>

  • ../trunk-jpl/externalpackages/dakota/configs/6.2-mpi/pecos_global_defs.hpp.patch

     
     124a25
     2> #ifndef PI
     325a27
     4> #endif

  • ../trunk-jpl/externalpackages/dakota/install-6.1-mpi-macosx64-yosemite.sh

     
    2828patch $DAK_SRC/CMakeLists.txt configs/6.1-mpi/CMakeLists.txt.patch
    2929
    3030#Apply patches
    31 patch src/src/ParallelLibrary.cpp configs/6.1/ParallelLibrary.cpp.patch
    32 patch src/src/ParallelLibrary.hpp configs/6.1/ParallelLibrary.hpp.patch
    33 patch src/src/NonDSampling.cpp configs/6.1/NonDSampling.cpp.patch
    34 patch src/src/NonDLocalReliability.cpp configs/6.1/NonDLocalReliability.cpp.patch
    35 patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.1/pecos_global_defs.hpp.patch
     31patch src/src/ParallelLibrary.cpp configs/6.1-mpi/ParallelLibrary.cpp.patch
     32patch src/src/ParallelLibrary.hpp configs/6.1-mpi/ParallelLibrary.hpp.patch
     33patch src/src/NonDSampling.cpp configs/6.1-mpi/NonDSampling.cpp.patch
     34patch src/src/NonDLocalReliability.cpp configs/6.1-mpi/NonDLocalReliability.cpp.patch
     35patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.1-mpi/pecos_global_defs.hpp.patch
    3636
    3737#Configure dakota
    3838cd $DAK_BUILD

  • ../trunk-jpl/externalpackages/dakota/install-6.2-mpi-macosx64-yosemite.sh

     
     1#!/bin/bash
     2set -eu
     3
     4#Some cleanup
     5rm -rf Dakota
     6rm -rf src
     7rm -rf build
     8rm -rf install
     9mkdir src build install
     10
     11#Download from ISSM server
     12#$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.1-public.src.tar.gz' 'dakota-6.1-public-src.tar.gz'
     13
     14#Untar
     15tar -zxvf dakota-6.2-public.src.tar.gz
     16
     17#Move Dakota to src directory
     18mv dakota-6.2.0.src/* src
     19rm -rf dakota-6.2.0.src
     20
     21#Set up Dakota cmake variables and config
     22export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src
     23export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
     24export MPIHOME=$ISSM_DIR/externalpackages/mpich/install
     25cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
     26patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2-mpi/BuildDakotaCustom.cmake.yosemite.patch
     27patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2-mpi/DakotaDev.cmake.patch
     28patch $DAK_SRC/CMakeLists.txt configs/6.2-mpi/CMakeLists.txt.patch
     29
     30#Apply patches
     31patch src/src/NonDSampling.cpp configs/6.2-mpi/NonDSampling.cpp.patch
     32patch src/src/NonDLocalReliability.cpp configs/6.2-mpi/NonDLocalReliability.cpp.patch
     33patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2-mpi/pecos_global_defs.hpp.patch
     34
     35#Configure dakota
     36cd $DAK_BUILD
     37
     38cmake -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \
     39           -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \
     40           -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \
     41           -D LDFLAGS="-std=gnu++0x" \
     42                -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \
     43                -C $DAK_SRC/cmake/DakotaDev.cmake \
     44                $DAK_SRC
     45cd ..
     46
     47#Compile and install dakota
     48cd $DAK_BUILD
     49if [ $# -eq 0 ];
     50then
     51        make
     52        make install
     53else
     54        make -j $1
     55        make -j $1 install
     56fi
     57cd ..
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